Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 83 Profile

GeneModule member RegulatorRegulator MotifMotif
Network Help

A network view of the module is created using cytoscapeWeb and enables dynamic, interactive exploration of the module properties. In this view, module member genes, motifs, and regulatory influences are represented as peripheral nodes connected to core module node via edges.

Module members are green circles, regulators are red triangles and motifs are blue diamonds. Selection of a node gives access to detailed information in a pop-up window, which allows dragging and pinning to compare multiple selections. Selecting module members will show information about the selected gene such as name, species and fucntions. Motif selection will show motif logo image and e-values. Bicluster selction will show expression profile and summary statistics for the module.

GeneModule member RegulatorRegulator MotifMotif
Regulators for Module 83

There are 10 regulatory influences for Module 83

Regulator Table (10)
Regulator Name Type
DVU1063 tf
DVU2960 tf
DVU0946 tf
DVU0653 tf
DVU0110 tf
DVU1518
DVU3066		 combiner
DVU0749
DVU0110		 combiner
DVU0744
DVU0946		 combiner
DVU0653
DVU2960		 combiner
DVU3111
DVU0946		 combiner

Regulator Help

For each module, single or AND logic connected regulatory influences are listed under the regulators tab. These regulatory influences are identified by Inferelator. Table shows name of the regulator and its type.

tf: Transcription factor

ef: Environmental factor

combiner: Combinatorial influence of a tf or an ef through logic gate. Table is sortable by clicking on the arrows next to column headers.

Motif information (de novo identified motifs for modules)

There are 2 motifs predicted.
Click on the RegPredict links to explore the motif in RegPredict.

Motif Table (2)
Motif Id e-value Consensus Motif Logo RegPredict
163 1.20e+03 gcGgtgtcAtG
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 RegPredict
164 1.10e+04 TTcTTTAATTAAA
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 RegPredict
Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment

Regulon 83 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolic pathways kegg pathway 1.19e-02 2.01e-02 8/31
Carbohydrate Metabolism kegg subcategory 1.61e-03 1.01e-02 6/31
Metabolism of Cofactors and Vitamins kegg subcategory 1.62e-02 4.83e-02 3/31
Metabolism kegg subcategory 2.21e-03 1.25e-02 13/31
Metabolism kegg category 5.93e-04 5.55e-03 15/31
Global kegg category 2.21e-03 1.58e-02 13/31
Carbohydrate Metabolism kegg subcategory 2.33e-02 4.75e-02 3/31
Metabolism of Cofactors and Vitamins kegg subcategory 1.57e-02 3.57e-02 3/31
Global kegg category 1.39e-02 3.29e-02 8/31
Metabolism kegg subcategory 1.39e-02 3.29e-02 8/31
Metabolic pathways kegg pathway 1.19e-02 2.95e-02 8/31

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
two-component signal transduction system (phosphorelay) biological_process 4.52e-03 7.92e-03 4/31
regulation of transcription, DNA-dependent biological_process 3.30e-02 4.45e-02 4/31
metabolic process biological_process 2.46e-02 3.42e-02 3/31
two-component response regulator activity molecular_function 1.02e-03 2.03e-03 4/31

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 1.82e-02 3.00e-02 10/31
Signal transduction mechanisms cog subcategory 2.08e-02 3.38e-02 5/31
Cell wall/membrane/envelope biogenesis cog subcategory 1.08e-02 1.85e-02 4/31
Carbohydrate transport and metabolism cog subcategory 8.24e-03 1.44e-02 3/31
Functions Help

Biological networks contain sets of regulatory units called functional modules that together play a role in regulation of specific functional processes. Connections between different modules in the network can help identify regulatory relationships such as hierarchy and epistasis. In addition, associating functions with modules enables putative assignment of functions to hypothetical genes. It is therefore essential to identify functional enrichment of modules within the regulatory network.

Functional annotations from single sources are often either not available or not complete. Therefore, we integrated KEGG pathway, Gene Ontology, TIGRFam and COG information as references for functional enrichment analysis.

We use hypergeometric p-values to identify significant overlaps between co-regulated module members and genes assigned to a particular functional annotation category. P-values are corrected for multiple comparisons by using Benjamini-Hochberg correction and filtered for p-values ≤ 0.05.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Members for Module 83

There are 31 genes in Module 83

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0005 CDS 2794228 chromosome 7835 8620 + lipoprotein False
DVU0082 CDS 2796749 chromosome 100383 101975 - hypothetical protein DVU0082 False
DVU0258 CDS 2794100 chromosome 301447 303420 - sensory box histidine kinase/response regulator False
DVU0271 CDS 2794325 chromosome 313230 314720 + response regulator False
DVU0635 CDS 2794105 chromosome 702696 704282 - dolichyl-phosphate-mannose-protein mannosyltransferase family protein False
DVU0652 cheV-2 CDS 2795042 chromosome 723349 724299 + chemotaxis protein CheV False
DVU0686 CDS 2795336 chromosome 760765 761253 + iron-sulfur cluster-binding protein False
DVU0742 CDS 2795258 chromosome 829630 830466 + hypothetical protein DVU0742 False
DVU0946 CDS 2794590 chromosome 1039992 1041422 + sigma-54 dependent transcriptional regulator/response regulator True
DVU0947 CDS 2794591 chromosome 1041478 1042383 - hypothetical protein DVU0947 False
DVU0969 CDS 2794471 chromosome 1066264 1067010 + amino acid transporter LysE False
DVU0973 CDS 2795105 chromosome 1069632 1070501 + 4-hydroxybenzoate octaprenyltransferase False
DVU0998 CDS 2795112 chromosome 1092123 1093178 + heptosyltransferase family protein False
DVU1007 cobU CDS 2794645 chromosome 1102911 1103447 + cobinamide kinase/cobinamide phosphate guanylyltransferase False
DVU2244 glgA CDS 2795396 chromosome 2338679 2340148 - glycogen synthase False
DVU2357 CDS 2796516 chromosome 2455000 2456109 - HD domain-containing protein False
DVU2418 CDS 2794359 chromosome 2525837 2526259 - vanZ-like family protein False
DVU2635 CDS 2795252 chromosome 2750041 2751174 + glycosyl transferase group 1 family protein False
DVU2638 CDS 2795694 chromosome 2754320 2755408 - hypothetical protein DVU2638 False
DVU2759 CDS 2794032 chromosome 2868041 2868187 - hypothetical protein DVU2759 False
DVU2900 CDS 2793930 chromosome 2999180 3000379 + amidohydrolase family protein False
DVU2905 CDS 2793935 chromosome 3006122 3007300 - iron-containing alcohol dehydrogenase False
DVU2976 CDS 2796290 chromosome 3084007 3085119 - hypothetical protein DVU2976 False
DVU2993 CDS 2796307 chromosome 3101540 3104203 + glycosyl transferase group 1/2 family protein False
DVU3015 CDS 2793728 chromosome 3130655 3131221 + hypothetical protein DVU3015 False
DVU3086 cobB-2 CDS 2796437 chromosome 3227312 3229135 + cobyrinic acid a,c-diamide synthase False
DVU3222 pgi CDS 2796220 chromosome 3391257 3392600 - glucose-6-phosphate isomerase False
DVU3224 sfsA CDS 2793874 chromosome 3394126 3394854 + sugar fermentation stimulation protein False
DVU3278 CDS 2796002 chromosome 3452517 3454073 - peptidase/PDZ domain-containing protein False
DVU3295 CDS 2796019 chromosome 3473090 3473737 - hemolysin III False
DVU3320 CDS 2796056 chromosome 3498575 3498955 - hypothetical protein DVU3320 False

Genes Help

Gene member table shows all the genes included in the module. Listed attributes are;

  1. Name: Gene name or Locus tag
  2. Common Name: Gene short name
  3. Type: Type of the feature, usually CDS.
  4. Gene ID: Link to NCBI Gene ID
  5. Chromosome: Chromosome name from annotation file
  6. Start/End:Feature start and end coordinates
  7. Strand: strand of the gene
  8. Description: Description of the gene from annotation file
  9. TF: If the gene is a Transcription Factor or not.

If you are browsing the Network Portal by using Gaggle/Firegoose, firegoose plugin will capture the NameList of the gene members. Captured names can be saved into your Workspace by clicking on "Capture" in the firegoose toolbar or can be directly sent other desktop and web resources by using "Broadcast" option.

Help

What is a module?

Regulatory units (modules) in the Network Portal are based on the network inference algorithm used. For the current version, modules are based on cMonkey modules and Inferelator regulatory influences on these modules. More specifically, module refers to set of genes that are conditionally co-regulated under subset of the conditions. Identification of modules integrates co-expression, de-novo motif identification, and other functional associations such as operon information and protein-protein interactions.

Module Overview

The landing module page shows quick summary info including co-expression profiles, de-novo identified motifs, and transcription factors and/or environmental factors as regulatory influences. It also includes module residual, motif e-values, conditions and links to other resources such as NCBI and Microbesonline. . If a transcription factor is included in the manually curated RegPrecise database, further information from RegPrecise is shown, allowing users to perform comparative analysis.

Expression Profiles

Expression profiles is a plot of the expression ratios (log10) of the module's genes, over all subset of the conditions included in the module. The X-axis represent conditions and the Y-axis represents log10 expression ratios. Each gene is plotted as line plot with different colors. Colored legend for the lines are presented under the plot. This plot is dynamic. Clicking on the gene names in the legend will show/hide the plot for that particular gene. A tooltip will show expression ratio information if you mouseover the lines in the plot.

Motif Locations

Location of the Identified motifs for the module in the upstream regions of the member genes are shown under the expression profiles plot. This plot shows the diagram of the upstream positions of the motifs, colored red and green for motifs #1, and 2, respectively. Intensity of the color is proportional to the significance of the occurence of that motif at a given location. Motifs on the forward and reverse strand are represented over and under the line respectively.

Network

A network view of the module is created using cytoscapeWeb and enables dynamic, interactive exploration of the module properties. In this view, module member genes, motifs, and regulatory influences are represented as peripheral nodes connected to core module node via edges. Module members are green circles, regulators are red triangles and motifs are blue diamonds. Selection of a node gives access to detailed information in a pop-up window, which allows dragging and pinning to compare multiple selections. Selecting module members will show information about the selected gene such as name, species and fucntions. Motif selection will show motif logo image and e-values. Bicluster selction will show expression profile and summary statistics for the module.

GeneModule member RegulatorRegulator MotifMotif

Regulators

For each module, single or AND logic connected regulatory influences are listed under the regulators tab. These regulatory influences are identified by Inferelator. Table shows name of the regulator and its type. tf: Transcription factor, ef: Environmental factor and combiner:Combinatorial influence of a tf or an ef through logic gate. Tabel is sortable by clicking on the arrows next to column headers.

Motifs

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Functions

Biological networks contain sets of regulatory units called functional modules that together play a role in regulation of specific functional processes. Connections between different modules in the network can help identify regulatory relationships such as hierarchy and epistasis. In addition, associating functions with modules enables putative assignment of functions to hypothetical genes. It is therefore essential to identify functional enrichment of modules within the regulatory network.

Functional annotations from single sources are often either not available or not complete. Therefore, we integrated KEGG pathway, Gene Ontology, TIGRFam and COG information as references for functional enrichment analysis.

We use hypergeometric p-values to identify significant overlaps between co-regulated module members and genes assigned to a particular functional annotation category. P-values are corrected for multiple comparisons by using Benjamini-Hochberg correction and filtered for p-values ≤ 0.05.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Genes

Gene member table shows all the genes included in the module. Listed attributes are;

  1. Name: Gene name or Locus tag
  2. Common Name: Gene short name
  3. Type: Type of the feature, usually CDS.
  4. Gene ID: Link to NCBI Gene ID
  5. Chromosome: Chromosome name from annotation file
  6. Start/End:Feature start and end coordinates
  7. Strand: strand of the gene
  8. Description: Description of the gene from annotation file
  9. TF: If the gene is a Transcription Factor or not.

If you are browsing the Network Portal by using Gaggle/Firegoose, firegoose plugin will capture the NameList of the gene members. Captured names can be saved into your Workspace by clicking on "Capture" in the firegoose toolbar or can be directly sent other desktop and web resources by using "Broadcast" option.

Social

You can start a conversation about this module or join the existing discussion by adding your comments. In order to be able to add your comments you need to sign in by using any of the following services;Disqus, Google, Facebook or Twitter. For full compatibility with other network portal features, we recommend using your Google ID.

Definitions

Residual: is a measure of bicluster quality. Mean bicluster residual is smaller when the expression profile of the genes in the module is "tighter". So smaller residuals are usually indicative of better bicluster quality.

Expression Profile: is a preview of the expression profiles of all the genes under subset of conditions included in the module. Tighter expression profiles are usually indicative of better bicluster quality.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Genes: Number of genes included in the module.

Functions: We identify functional enrichment of each module by camparing to different functional categories such as KEGG, COG, GO etc. by using hypergeometric function. If the module is significantly enriched for any of the functions, this column will list few of the these functions as an overview. Full list of functions is available upon visiting the module page under the Functions tab.